Multiple sequence alignment - TraesCS2D01G306100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G306100 chr2D 100.000 6078 0 0 1 6078 391725390 391719313 0.000000e+00 11225.0
1 TraesCS2D01G306100 chr2D 86.111 144 19 1 325 468 183381664 183381806 2.930000e-33 154.0
2 TraesCS2D01G306100 chr2D 95.402 87 3 1 5877 5963 582150571 582150486 2.950000e-28 137.0
3 TraesCS2D01G306100 chr2A 95.539 3183 69 26 2709 5871 528661700 528658571 0.000000e+00 5024.0
4 TraesCS2D01G306100 chr2A 93.771 2713 120 26 44 2711 528664665 528661957 0.000000e+00 4028.0
5 TraesCS2D01G306100 chr2A 87.611 113 4 3 5970 6078 528658570 528658464 8.270000e-24 122.0
6 TraesCS2D01G306100 chr2B 94.070 2479 106 15 789 3256 463286493 463284045 0.000000e+00 3725.0
7 TraesCS2D01G306100 chr2B 92.039 2173 109 34 3258 5393 463283916 463281771 0.000000e+00 2996.0
8 TraesCS2D01G306100 chr2B 86.393 779 84 11 1 771 463287442 463286678 0.000000e+00 832.0
9 TraesCS2D01G306100 chr2B 90.948 232 6 7 5609 5838 463281628 463281410 1.280000e-76 298.0
10 TraesCS2D01G306100 chr2B 100.000 28 0 0 5447 5474 463281738 463281711 1.100000e-02 52.8
11 TraesCS2D01G306100 chrUn 100.000 411 0 0 3615 4025 477664818 477665228 0.000000e+00 760.0
12 TraesCS2D01G306100 chr5B 92.708 96 5 2 5862 5955 603648387 603648292 2.950000e-28 137.0
13 TraesCS2D01G306100 chr5A 92.632 95 5 2 5863 5955 25093740 25093834 1.060000e-27 135.0
14 TraesCS2D01G306100 chr5A 93.333 90 4 2 5880 5968 324692642 324692554 1.370000e-26 132.0
15 TraesCS2D01G306100 chr6B 90.291 103 7 3 5862 5962 342268487 342268386 1.370000e-26 132.0
16 TraesCS2D01G306100 chr4D 91.579 95 6 2 5863 5955 270678642 270678548 4.940000e-26 130.0
17 TraesCS2D01G306100 chr1B 90.909 99 6 3 5859 5954 33741296 33741394 4.940000e-26 130.0
18 TraesCS2D01G306100 chr1B 89.524 105 5 5 5868 5968 654313573 654313675 1.780000e-25 128.0
19 TraesCS2D01G306100 chr3B 89.899 99 9 1 5880 5978 818896663 818896566 6.400000e-25 126.0
20 TraesCS2D01G306100 chr3D 84.694 98 9 3 375 467 39545786 39545690 6.490000e-15 93.5
21 TraesCS2D01G306100 chr3A 83.673 98 11 1 375 467 51296091 51295994 3.020000e-13 87.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G306100 chr2D 391719313 391725390 6077 True 11225.00 11225 100.000 1 6078 1 chr2D.!!$R1 6077
1 TraesCS2D01G306100 chr2A 528658464 528664665 6201 True 3058.00 5024 92.307 44 6078 3 chr2A.!!$R1 6034
2 TraesCS2D01G306100 chr2B 463281410 463287442 6032 True 1580.76 3725 92.690 1 5838 5 chr2B.!!$R1 5837

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
736 773 0.392706 TTGTCCTCAGATGCACGTGT 59.607 50.000 18.38 0.0 0.0 4.49 F
1387 1596 0.668096 CCAATCCGTTTCCGTCGACA 60.668 55.000 17.16 0.0 0.0 4.35 F
2973 3451 1.067212 GTGGGAGGTGTGAGCGTATAG 59.933 57.143 0.00 0.0 0.0 1.31 F
4206 4831 1.037579 GGGGTGGCCATGCTAGAAAC 61.038 60.000 9.72 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2483 1.063417 CAATCTCCCCCTCAGCCAAAT 60.063 52.381 0.00 0.0 0.00 2.32 R
3370 3979 1.546476 GGAGGAGCCATCATAGGTACG 59.454 57.143 0.00 0.0 36.34 3.67 R
4261 4886 0.034616 AGAACAGCAGGTGTCAGCTC 59.965 55.000 5.53 0.0 39.03 4.09 R
6001 6658 0.523519 TGCAGACAGAGCAGTCGTAG 59.476 55.000 0.00 0.0 43.24 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.468072 CAGAGCTTCTTAGTTGTGTGATTGT 59.532 40.000 0.00 0.00 0.00 2.71
35 36 6.543831 AGAGCTTCTTAGTTGTGTGATTGTTT 59.456 34.615 0.00 0.00 0.00 2.83
40 41 6.969366 TCTTAGTTGTGTGATTGTTTCATGG 58.031 36.000 0.00 0.00 36.54 3.66
42 43 3.321682 AGTTGTGTGATTGTTTCATGGGG 59.678 43.478 0.00 0.00 36.54 4.96
85 86 2.679082 TCCCTCAAGAGCTACCATACC 58.321 52.381 0.00 0.00 0.00 2.73
160 165 2.022129 GTCGTGGGAGCAGTCGTTG 61.022 63.158 0.00 0.00 0.00 4.10
161 166 2.029073 CGTGGGAGCAGTCGTTGT 59.971 61.111 0.00 0.00 0.00 3.32
166 171 3.550656 GAGCAGTCGTTGTTCCCG 58.449 61.111 0.00 0.00 31.42 5.14
218 225 7.250569 CAAAAGTGTGAACTTGAGTGTACATT 58.749 34.615 0.00 0.00 30.89 2.71
221 228 7.391148 AGTGTGAACTTGAGTGTACATTTTT 57.609 32.000 0.00 0.00 30.89 1.94
261 268 7.649306 TCGGTTGTCTCTTAACACTAACTTTAC 59.351 37.037 0.00 0.00 0.00 2.01
262 269 7.095899 CGGTTGTCTCTTAACACTAACTTTACC 60.096 40.741 0.00 0.00 0.00 2.85
264 271 9.322773 GTTGTCTCTTAACACTAACTTTACCTT 57.677 33.333 0.00 0.00 0.00 3.50
292 299 8.364142 TGTTATTACTTGCTTATTTGTTGCCTT 58.636 29.630 0.00 0.00 0.00 4.35
297 304 3.129871 TGCTTATTTGTTGCCTTTGTGC 58.870 40.909 0.00 0.00 0.00 4.57
424 431 9.623000 AAGTATTAAATTTGGTAGTCGCCTATT 57.377 29.630 0.00 0.00 0.00 1.73
425 432 9.052759 AGTATTAAATTTGGTAGTCGCCTATTG 57.947 33.333 0.00 0.00 0.00 1.90
468 475 2.093288 AGCGCATCTTTGATCCTTCAGA 60.093 45.455 11.47 0.00 32.27 3.27
560 567 1.038130 ATCCTCCTCAAGGTCGTCCG 61.038 60.000 0.00 0.00 46.32 4.79
629 664 2.202703 GGCGCCGACGATGTTAGT 60.203 61.111 12.58 0.00 43.93 2.24
634 669 1.058695 CGCCGACGATGTTAGTGTTTC 59.941 52.381 0.00 0.00 43.93 2.78
635 670 2.334838 GCCGACGATGTTAGTGTTTCT 58.665 47.619 0.00 0.00 0.00 2.52
636 671 2.344741 GCCGACGATGTTAGTGTTTCTC 59.655 50.000 0.00 0.00 0.00 2.87
637 672 3.571571 CCGACGATGTTAGTGTTTCTCA 58.428 45.455 0.00 0.00 0.00 3.27
638 673 3.985279 CCGACGATGTTAGTGTTTCTCAA 59.015 43.478 0.00 0.00 0.00 3.02
639 674 4.446385 CCGACGATGTTAGTGTTTCTCAAA 59.554 41.667 0.00 0.00 0.00 2.69
641 676 5.175126 CGACGATGTTAGTGTTTCTCAAAGT 59.825 40.000 0.00 0.00 0.00 2.66
642 677 6.287107 ACGATGTTAGTGTTTCTCAAAGTG 57.713 37.500 0.00 0.00 0.00 3.16
643 678 5.140177 CGATGTTAGTGTTTCTCAAAGTGC 58.860 41.667 0.00 0.00 0.00 4.40
649 685 2.080693 TGTTTCTCAAAGTGCGTGTGT 58.919 42.857 0.00 0.00 0.00 3.72
655 691 2.534019 AAAGTGCGTGTGTGCGAGG 61.534 57.895 0.00 0.00 37.81 4.63
660 696 1.163420 TGCGTGTGTGCGAGGAAAAT 61.163 50.000 0.00 0.00 37.81 1.82
704 741 2.821969 GGGTTCAATGACAATGACTGCT 59.178 45.455 0.00 0.00 0.00 4.24
736 773 0.392706 TTGTCCTCAGATGCACGTGT 59.607 50.000 18.38 0.00 0.00 4.49
750 787 3.013276 CACGTGTGCTAAGACTTCTCA 57.987 47.619 7.58 0.00 0.00 3.27
770 941 6.325596 TCTCAACTGTCATCGACAAGATAAG 58.674 40.000 0.00 0.00 42.26 1.73
843 1048 2.258013 CGTTTCAAGCGAAGGGGCA 61.258 57.895 0.00 0.00 34.64 5.36
911 1118 9.419297 GAGGAACAAGGTGGATTTAAAATAAAC 57.581 33.333 0.00 0.00 0.00 2.01
941 1149 4.762289 AACCTAGATCTTGTCACATCCC 57.238 45.455 0.00 0.00 0.00 3.85
973 1182 0.762461 CCCCCTCCTCTGTCATCTCC 60.762 65.000 0.00 0.00 0.00 3.71
992 1201 1.720694 CCTCGCGGTCTTCTCCTCTC 61.721 65.000 6.13 0.00 0.00 3.20
993 1202 1.720694 CTCGCGGTCTTCTCCTCTCC 61.721 65.000 6.13 0.00 0.00 3.71
1387 1596 0.668096 CCAATCCGTTTCCGTCGACA 60.668 55.000 17.16 0.00 0.00 4.35
1419 1628 1.227497 GATCTTGCCTCCTCTGCCG 60.227 63.158 0.00 0.00 0.00 5.69
1472 1685 4.262249 GGGTTTTGTTGATTCGGGAATTCA 60.262 41.667 7.93 0.00 0.00 2.57
1474 1687 5.508994 GGTTTTGTTGATTCGGGAATTCAGT 60.509 40.000 7.93 0.00 0.00 3.41
1591 1804 3.406152 AGGAGTATGACCTGATATCCCCA 59.594 47.826 0.00 0.00 36.30 4.96
1626 1839 6.424509 TCGATTCAATTTGCTTGATTTGCTTT 59.575 30.769 0.00 0.00 43.30 3.51
1628 1841 8.222433 CGATTCAATTTGCTTGATTTGCTTTAA 58.778 29.630 0.00 0.00 43.30 1.52
1760 1973 7.710907 CAGTTTCCAAGTATTAGCAGCAGTATA 59.289 37.037 0.00 0.00 0.00 1.47
1778 1991 7.766278 AGCAGTATAATCACACGAGATTTTTCT 59.234 33.333 7.55 2.56 38.97 2.52
1893 2106 8.295288 GTGTGAGCTAGTTCTAAAGTTACAGTA 58.705 37.037 8.15 0.00 0.00 2.74
1926 2139 3.346315 GCTTGCCAGCCCAATAAATTTT 58.654 40.909 0.00 0.00 40.61 1.82
1932 2145 6.897986 TGCCAGCCCAATAAATTTTATCATT 58.102 32.000 0.00 0.00 0.00 2.57
1965 2178 6.966632 CAGTTTTTCATATGGGTGATTACACG 59.033 38.462 2.13 0.00 46.77 4.49
1987 2200 2.483877 CGCTGTTGGATGCAACTTTCTA 59.516 45.455 27.36 8.96 36.15 2.10
2013 2226 1.208293 AGCCTTCTTTGGTCGATCCTC 59.792 52.381 0.00 0.00 37.07 3.71
2092 2305 3.149196 TGTCCTTTCTGTCCTTCAATGC 58.851 45.455 0.00 0.00 0.00 3.56
2158 2372 7.759465 TCTGAGTATTTAGTGTGTACTGCTAC 58.241 38.462 0.00 0.00 37.78 3.58
2269 2483 3.141398 GTCAGCTTGATGAGACCACAAA 58.859 45.455 0.00 0.00 0.00 2.83
2329 2543 8.450964 CACAATATCCGTATTTTTGTCAGACTT 58.549 33.333 1.31 0.00 0.00 3.01
2343 2557 4.709397 TGTCAGACTTGGAAACATGGTTTT 59.291 37.500 0.00 0.00 42.32 2.43
2457 2672 9.118300 GTGAAATGATCCTCTTCACTTCATTAT 57.882 33.333 17.78 0.00 41.97 1.28
2469 2684 7.543520 TCTTCACTTCATTATAGATGCATAGCG 59.456 37.037 0.00 0.00 0.00 4.26
2563 2778 6.426587 ACATTTACCATTCAGGACTGCTAAT 58.573 36.000 0.00 0.00 41.22 1.73
2688 2903 6.804677 TGTTCAAGAGTGTGCAATTGTAATT 58.195 32.000 7.40 0.00 0.00 1.40
2920 3398 8.877808 TTGTACACAGATTGCTGATTAGATAG 57.122 34.615 0.00 0.00 45.17 2.08
2973 3451 1.067212 GTGGGAGGTGTGAGCGTATAG 59.933 57.143 0.00 0.00 0.00 1.31
3370 3979 4.974721 CCACCACCACCACTGGGC 62.975 72.222 0.00 0.00 42.74 5.36
3430 4039 7.015195 AGAGGTTTTGCTGGTAATTAACACATT 59.985 33.333 0.00 0.00 0.00 2.71
3431 4040 6.928492 AGGTTTTGCTGGTAATTAACACATTG 59.072 34.615 0.00 0.00 0.00 2.82
3457 4066 8.846211 GGCTATACCATTCACTATTGCTTTTTA 58.154 33.333 0.00 0.00 38.86 1.52
4150 4774 7.337938 TGAATAATCAAATGTGTGCCTAGAGA 58.662 34.615 0.00 0.00 30.99 3.10
4206 4831 1.037579 GGGGTGGCCATGCTAGAAAC 61.038 60.000 9.72 0.00 0.00 2.78
4261 4886 2.459060 TGGTCATGCCATTTTTGCTG 57.541 45.000 4.93 0.00 43.61 4.41
4270 4895 2.669364 CCATTTTTGCTGAGCTGACAC 58.331 47.619 5.83 0.00 0.00 3.67
4426 5062 0.532862 ACTCCACAACAGCGACAAGG 60.533 55.000 0.00 0.00 0.00 3.61
4462 5098 6.681729 AGGTTTAGTGTTCTGGAGTATCAA 57.318 37.500 0.00 0.00 36.25 2.57
4890 5533 1.723003 GCTTTGCTGATTTCGCCTTTG 59.277 47.619 0.00 0.00 0.00 2.77
4989 5633 0.944386 TTGTTTCCTCAGTCTTGCGC 59.056 50.000 0.00 0.00 0.00 6.09
5121 5768 4.180057 CCTCACAAAGTGCTATGTCTCTC 58.820 47.826 0.00 0.00 32.98 3.20
5192 5841 2.663826 ACTTGACTCAGCTTCGGATC 57.336 50.000 0.00 0.00 0.00 3.36
5279 5929 0.238289 TTAGCTGCGAGTTGCTTTGC 59.762 50.000 3.50 5.77 46.63 3.68
5320 5970 8.691661 AATCTTGTTTACCATCAGTTGTAACT 57.308 30.769 0.00 0.00 40.60 2.24
5333 5983 3.877508 AGTTGTAACTCTTCACACTTGGC 59.122 43.478 0.00 0.00 32.86 4.52
5368 6023 1.190323 CGCCGCGATCTAGTTCAAATC 59.810 52.381 8.23 0.00 0.00 2.17
5418 6073 3.763360 CCTGGTGCCAAAAATACATCTGA 59.237 43.478 0.00 0.00 0.00 3.27
5421 6076 4.021544 TGGTGCCAAAAATACATCTGAACC 60.022 41.667 0.00 0.00 0.00 3.62
5422 6077 4.021544 GGTGCCAAAAATACATCTGAACCA 60.022 41.667 0.00 0.00 0.00 3.67
5423 6078 5.337491 GGTGCCAAAAATACATCTGAACCAT 60.337 40.000 0.00 0.00 0.00 3.55
5424 6079 5.807011 GTGCCAAAAATACATCTGAACCATC 59.193 40.000 0.00 0.00 0.00 3.51
5425 6080 5.105392 TGCCAAAAATACATCTGAACCATCC 60.105 40.000 0.00 0.00 0.00 3.51
5430 6085 7.636150 AAAATACATCTGAACCATCCTTGAG 57.364 36.000 0.00 0.00 0.00 3.02
5432 6087 2.306805 ACATCTGAACCATCCTTGAGCA 59.693 45.455 0.00 0.00 0.00 4.26
5433 6088 2.479566 TCTGAACCATCCTTGAGCAC 57.520 50.000 0.00 0.00 0.00 4.40
5434 6089 1.699083 TCTGAACCATCCTTGAGCACA 59.301 47.619 0.00 0.00 0.00 4.57
5435 6090 1.808945 CTGAACCATCCTTGAGCACAC 59.191 52.381 0.00 0.00 0.00 3.82
5494 6149 2.996249 TGAAATTGCCAACAAAGCCA 57.004 40.000 0.00 0.00 39.77 4.75
5508 6163 5.021033 ACAAAGCCAAATGACATTGTTCA 57.979 34.783 0.34 0.00 0.00 3.18
5604 6259 2.616960 CGTAGCTTTGTGCATCTACCA 58.383 47.619 0.00 0.00 45.94 3.25
5606 6261 3.246226 CGTAGCTTTGTGCATCTACCATC 59.754 47.826 0.00 0.00 45.94 3.51
5731 6386 1.950909 GAGGACCAGTCGACCAGATAG 59.049 57.143 13.01 0.00 0.00 2.08
5790 6447 2.232941 TCCGTTTTATCGCTCCAGTCTT 59.767 45.455 0.00 0.00 0.00 3.01
5859 6516 7.045416 TCATGACTATAAATAAACAGTGGCGT 58.955 34.615 0.00 0.00 0.00 5.68
5871 6528 6.751514 AAACAGTGGCGTGATTTATCATAA 57.248 33.333 0.00 0.00 39.30 1.90
5872 6529 5.734855 ACAGTGGCGTGATTTATCATAAC 57.265 39.130 0.00 0.00 39.30 1.89
5873 6530 5.428253 ACAGTGGCGTGATTTATCATAACT 58.572 37.500 0.00 0.00 39.30 2.24
5874 6531 5.523916 ACAGTGGCGTGATTTATCATAACTC 59.476 40.000 0.00 0.00 39.30 3.01
5875 6532 5.755375 CAGTGGCGTGATTTATCATAACTCT 59.245 40.000 0.00 0.00 39.30 3.24
5876 6533 6.258727 CAGTGGCGTGATTTATCATAACTCTT 59.741 38.462 0.00 0.00 39.30 2.85
5877 6534 6.480320 AGTGGCGTGATTTATCATAACTCTTC 59.520 38.462 0.00 0.00 39.30 2.87
5878 6535 6.480320 GTGGCGTGATTTATCATAACTCTTCT 59.520 38.462 0.00 0.00 39.30 2.85
5879 6536 6.479990 TGGCGTGATTTATCATAACTCTTCTG 59.520 38.462 0.00 0.00 39.30 3.02
5880 6537 6.480320 GGCGTGATTTATCATAACTCTTCTGT 59.520 38.462 0.00 0.00 39.30 3.41
5881 6538 7.652105 GGCGTGATTTATCATAACTCTTCTGTA 59.348 37.037 0.00 0.00 39.30 2.74
5882 6539 9.031360 GCGTGATTTATCATAACTCTTCTGTAA 57.969 33.333 0.00 0.00 39.30 2.41
5930 6587 9.817809 TCACTATTTTAATGATCTAAACGCTCT 57.182 29.630 0.00 0.00 0.00 4.09
5945 6602 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
5946 6603 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
5947 6604 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
5948 6605 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
5949 6606 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
5950 6607 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
5951 6608 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
5952 6609 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
5953 6610 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
5954 6611 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
5955 6612 8.995027 TTATATTAGTTTACGGAGGGAGTACA 57.005 34.615 0.00 0.00 0.00 2.90
5956 6613 5.848833 ATTAGTTTACGGAGGGAGTACAG 57.151 43.478 0.00 0.00 0.00 2.74
5957 6614 3.166560 AGTTTACGGAGGGAGTACAGT 57.833 47.619 0.00 0.00 0.00 3.55
5958 6615 4.307032 AGTTTACGGAGGGAGTACAGTA 57.693 45.455 0.00 0.00 0.00 2.74
5959 6616 4.864726 AGTTTACGGAGGGAGTACAGTAT 58.135 43.478 0.00 0.00 0.00 2.12
5960 6617 6.006275 AGTTTACGGAGGGAGTACAGTATA 57.994 41.667 0.00 0.00 0.00 1.47
5961 6618 6.426587 AGTTTACGGAGGGAGTACAGTATAA 58.573 40.000 0.00 0.00 0.00 0.98
5962 6619 6.891908 AGTTTACGGAGGGAGTACAGTATAAA 59.108 38.462 0.00 0.00 0.00 1.40
5963 6620 6.699575 TTACGGAGGGAGTACAGTATAAAC 57.300 41.667 0.00 0.00 0.00 2.01
5964 6621 4.864726 ACGGAGGGAGTACAGTATAAACT 58.135 43.478 0.00 0.00 35.91 2.66
5965 6622 6.006275 ACGGAGGGAGTACAGTATAAACTA 57.994 41.667 0.00 0.00 33.48 2.24
5966 6623 5.825151 ACGGAGGGAGTACAGTATAAACTAC 59.175 44.000 0.00 0.00 33.48 2.73
5967 6624 6.060788 CGGAGGGAGTACAGTATAAACTACT 58.939 44.000 0.00 0.00 33.48 2.57
6001 6658 1.212616 AGCTTATCGCGATGCAGAAC 58.787 50.000 31.05 13.98 45.59 3.01
6041 6702 4.628715 GCACAGATGAGGGGGAGAATTTTA 60.629 45.833 0.00 0.00 0.00 1.52
6051 6712 3.524541 GGGAGAATTTTACCGCGTAGAA 58.475 45.455 4.92 0.00 0.00 2.10
6052 6713 4.124970 GGGAGAATTTTACCGCGTAGAAT 58.875 43.478 4.92 2.24 0.00 2.40
6053 6714 4.210746 GGGAGAATTTTACCGCGTAGAATC 59.789 45.833 4.92 0.00 0.00 2.52
6054 6715 4.085210 GGAGAATTTTACCGCGTAGAATCG 60.085 45.833 4.92 0.00 0.00 3.34
6062 6723 1.904144 CGCGTAGAATCGGAGTTTCA 58.096 50.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.615289 ACAATCACACAACTAAGAAGCTCT 58.385 37.500 0.00 0.00 0.00 4.09
14 15 7.592533 CCATGAAACAATCACACAACTAAGAAG 59.407 37.037 0.00 0.00 41.93 2.85
19 20 4.522405 CCCCATGAAACAATCACACAACTA 59.478 41.667 0.00 0.00 41.93 2.24
33 34 3.117550 CCCTCACATATGACCCCATGAAA 60.118 47.826 10.38 0.00 34.31 2.69
35 36 2.057140 CCCTCACATATGACCCCATGA 58.943 52.381 10.38 0.36 34.31 3.07
40 41 1.477558 CCAAGCCCTCACATATGACCC 60.478 57.143 10.38 0.00 0.00 4.46
42 43 2.843701 CTCCAAGCCCTCACATATGAC 58.156 52.381 10.38 0.00 0.00 3.06
85 86 5.404366 TGGTCAACGAATAAGTTTTCTCTCG 59.596 40.000 0.00 0.00 34.68 4.04
160 165 1.202722 TCCACTGAAAAGGTCGGGAAC 60.203 52.381 0.00 0.00 36.88 3.62
161 166 1.071699 CTCCACTGAAAAGGTCGGGAA 59.928 52.381 0.00 0.00 36.88 3.97
166 171 6.107343 GGTACTAATCTCCACTGAAAAGGTC 58.893 44.000 0.00 0.00 0.00 3.85
264 271 8.983724 GGCAACAAATAAGCAAGTAATAACAAA 58.016 29.630 0.00 0.00 0.00 2.83
281 288 1.139455 AGCTGCACAAAGGCAACAAAT 59.861 42.857 1.02 0.00 44.40 2.32
424 431 7.165485 GCTAGATATCAACTAGAGGAGAGTCA 58.835 42.308 5.32 0.00 39.48 3.41
425 432 6.312918 CGCTAGATATCAACTAGAGGAGAGTC 59.687 46.154 5.32 0.00 39.48 3.36
507 514 2.000447 GCCAACTCGAAGATAAAGCGT 59.000 47.619 0.00 0.00 33.89 5.07
560 567 2.430921 CACCGACTCTGTGCCGAC 60.431 66.667 0.00 0.00 0.00 4.79
589 596 6.015772 GCCCTAAGAAGACACTAGGAATCTAG 60.016 46.154 0.00 0.00 46.38 2.43
629 664 2.080693 ACACACGCACTTTGAGAAACA 58.919 42.857 0.00 0.00 0.00 2.83
634 669 1.368019 CGCACACACGCACTTTGAG 60.368 57.895 0.00 0.00 0.00 3.02
635 670 1.761244 CTCGCACACACGCACTTTGA 61.761 55.000 0.00 0.00 0.00 2.69
636 671 1.368019 CTCGCACACACGCACTTTG 60.368 57.895 0.00 0.00 0.00 2.77
637 672 2.534019 CCTCGCACACACGCACTTT 61.534 57.895 0.00 0.00 0.00 2.66
638 673 2.916502 TTCCTCGCACACACGCACTT 62.917 55.000 0.00 0.00 0.00 3.16
639 674 2.916502 TTTCCTCGCACACACGCACT 62.917 55.000 0.00 0.00 0.00 4.40
641 676 1.163420 ATTTTCCTCGCACACACGCA 61.163 50.000 0.00 0.00 0.00 5.24
642 677 0.040425 AATTTTCCTCGCACACACGC 60.040 50.000 0.00 0.00 0.00 5.34
643 678 2.399396 AAATTTTCCTCGCACACACG 57.601 45.000 0.00 0.00 0.00 4.49
649 685 3.810310 AACACCAAAATTTTCCTCGCA 57.190 38.095 0.00 0.00 0.00 5.10
655 691 7.332182 TGTGAAACACCTAACACCAAAATTTTC 59.668 33.333 0.00 0.00 45.67 2.29
736 773 4.937201 TGACAGTTGAGAAGTCTTAGCA 57.063 40.909 0.00 0.00 33.56 3.49
748 785 6.267496 TCTTATCTTGTCGATGACAGTTGA 57.733 37.500 0.00 1.76 43.69 3.18
750 787 9.469807 GATTATCTTATCTTGTCGATGACAGTT 57.530 33.333 0.00 0.00 43.69 3.16
843 1048 5.103000 CGTCTCTGGTTTCATCGTTAATCT 58.897 41.667 0.00 0.00 0.00 2.40
1387 1596 2.271800 CAAGATCTCGCGCTTTTACCT 58.728 47.619 5.56 0.00 0.00 3.08
1439 1652 6.478344 CGAATCAACAAAACCCAAATCAGAAA 59.522 34.615 0.00 0.00 0.00 2.52
1472 1685 1.891450 CGTCACCTTGGAGTCCCTACT 60.891 57.143 6.74 0.00 39.21 2.57
1474 1687 0.613853 CCGTCACCTTGGAGTCCCTA 60.614 60.000 6.74 0.00 0.00 3.53
1579 1792 5.048504 CGAACAAAATCATGGGGATATCAGG 60.049 44.000 4.83 0.00 34.28 3.86
1591 1804 7.894376 AGCAAATTGAATCGAACAAAATCAT 57.106 28.000 11.30 0.00 0.00 2.45
1626 1839 4.696877 CAGACATCCACAGCTGAACAATTA 59.303 41.667 23.35 0.00 0.00 1.40
1628 1841 3.079578 CAGACATCCACAGCTGAACAAT 58.920 45.455 23.35 5.28 0.00 2.71
1727 1940 9.167311 CTGCTAATACTTGGAAACTGAACTATT 57.833 33.333 0.00 0.00 0.00 1.73
1778 1991 9.331466 AGGCAATCTGATCCTCTTATCTAAATA 57.669 33.333 0.00 0.00 0.00 1.40
1893 2106 1.372307 GGCAAGCCCAAACTGCAAT 59.628 52.632 0.00 0.00 0.00 3.56
1926 2139 5.000591 TGAAAAACTGAGCGGACAATGATA 58.999 37.500 0.00 0.00 0.00 2.15
1932 2145 3.689161 CCATATGAAAAACTGAGCGGACA 59.311 43.478 3.65 0.00 0.00 4.02
1987 2200 3.486383 TCGACCAAAGAAGGCTGAAATT 58.514 40.909 0.00 0.00 0.00 1.82
2013 2226 4.837896 TGATCTCAGCAACGACCTATAG 57.162 45.455 0.00 0.00 0.00 1.31
2158 2372 4.184629 ACATTAGCTAAACAGCTCTTCCG 58.815 43.478 10.85 0.00 45.00 4.30
2269 2483 1.063417 CAATCTCCCCCTCAGCCAAAT 60.063 52.381 0.00 0.00 0.00 2.32
2329 2543 6.680131 GCATCGATATGAAAACCATGTTTCCA 60.680 38.462 0.00 0.00 36.80 3.53
2343 2557 4.260985 ACCAACACAAAGCATCGATATGA 58.739 39.130 0.00 0.00 34.84 2.15
2392 2606 3.193479 GCTAAGGAACTGTTCATTTGGGG 59.807 47.826 23.14 13.09 40.86 4.96
2400 2615 4.381411 ACAAGACAGCTAAGGAACTGTTC 58.619 43.478 12.05 12.05 46.82 3.18
2457 2672 6.819397 ACTATACAGAACGCTATGCATCTA 57.181 37.500 0.19 0.00 0.00 1.98
2736 3210 4.707448 TGTGGACAGTTTTATGTGGTTGTT 59.293 37.500 0.00 0.00 32.25 2.83
2737 3211 4.274147 TGTGGACAGTTTTATGTGGTTGT 58.726 39.130 0.00 0.00 32.25 3.32
2738 3212 4.909696 TGTGGACAGTTTTATGTGGTTG 57.090 40.909 0.00 0.00 32.25 3.77
2920 3398 3.855858 TGGCAAACCTGTCAAGAAAAAC 58.144 40.909 0.00 0.00 33.09 2.43
2973 3451 4.123497 TGACATGAGTGTACCTACATGC 57.877 45.455 17.16 12.63 42.28 4.06
3370 3979 1.546476 GGAGGAGCCATCATAGGTACG 59.454 57.143 0.00 0.00 36.34 3.67
3431 4040 6.884280 AAAGCAATAGTGAATGGTATAGCC 57.116 37.500 0.00 0.00 37.90 3.93
3457 4066 7.093068 ACCAGTGTTTTCTTTCCCAATAAAACT 60.093 33.333 0.00 0.00 38.70 2.66
3613 4224 6.413783 TCCACTGTGTTCTTGTTATCTGTA 57.586 37.500 7.08 0.00 0.00 2.74
4150 4774 8.710749 ACATATAAATGTATCAAATGGTGCCT 57.289 30.769 0.00 0.00 44.66 4.75
4206 4831 7.406799 AAAATTGCAATCTTAGACCAAAACG 57.593 32.000 13.38 0.00 0.00 3.60
4261 4886 0.034616 AGAACAGCAGGTGTCAGCTC 59.965 55.000 5.53 0.00 39.03 4.09
4270 4895 6.707608 TCATATTACAGCATTAGAACAGCAGG 59.292 38.462 0.00 0.00 0.00 4.85
4426 5062 8.747471 AGAACACTAAACCTATCTAACAGGTAC 58.253 37.037 0.00 0.00 45.90 3.34
4462 5098 2.232696 GTCCCAACACCACAAACTTGTT 59.767 45.455 0.00 0.00 39.91 2.83
4536 5172 5.673514 TGCATTAGCTGAACATATGACAGA 58.326 37.500 26.00 13.66 42.74 3.41
4841 5481 3.875727 CTGACTCATTAGCCAATGGAGTG 59.124 47.826 2.05 0.00 41.66 3.51
5192 5841 1.734465 GAGTCCATTGTGAAGAAGGCG 59.266 52.381 0.00 0.00 0.00 5.52
5320 5970 1.211703 TGAACCAGCCAAGTGTGAAGA 59.788 47.619 0.00 0.00 0.00 2.87
5333 5983 1.699656 CGGCGCAGAAGATGAACCAG 61.700 60.000 10.83 0.00 0.00 4.00
5368 6023 7.758873 AACCAGGAAATCCAATGATGGTTCAG 61.759 42.308 14.18 0.00 42.43 3.02
5418 6073 1.237285 GCGTGTGCTCAAGGATGGTT 61.237 55.000 3.95 0.00 38.39 3.67
5430 6085 1.290955 TGGTAGTACCAGCGTGTGC 59.709 57.895 18.45 0.00 44.79 4.57
5508 6163 4.386652 GCAATTTGATGCATGTTCTTTCGT 59.613 37.500 2.46 0.00 45.70 3.85
5590 6245 3.365868 GCAAACGATGGTAGATGCACAAA 60.366 43.478 0.00 0.00 33.25 2.83
5708 6363 1.152631 TGGTCGACTGGTCCTCACA 60.153 57.895 16.46 0.00 0.00 3.58
5731 6386 1.648467 GCCAGGCGAACCAGACAATC 61.648 60.000 0.00 0.00 39.06 2.67
5790 6447 3.534357 TGCCAAAACAAATAGAGGGGA 57.466 42.857 0.00 0.00 0.00 4.81
5904 6561 9.817809 AGAGCGTTTAGATCATTAAAATAGTGA 57.182 29.630 0.00 0.00 37.82 3.41
5919 6576 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
5920 6577 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
5921 6578 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
5922 6579 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
5923 6580 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
5924 6581 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
5925 6582 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
5926 6583 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
5927 6584 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
5928 6585 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
5929 6586 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
5930 6587 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
5931 6588 8.220559 ACTGTACTCCCTCCGTAAACTAATATA 58.779 37.037 0.00 0.00 0.00 0.86
5932 6589 7.065504 ACTGTACTCCCTCCGTAAACTAATAT 58.934 38.462 0.00 0.00 0.00 1.28
5933 6590 6.426587 ACTGTACTCCCTCCGTAAACTAATA 58.573 40.000 0.00 0.00 0.00 0.98
5934 6591 5.267587 ACTGTACTCCCTCCGTAAACTAAT 58.732 41.667 0.00 0.00 0.00 1.73
5935 6592 4.666512 ACTGTACTCCCTCCGTAAACTAA 58.333 43.478 0.00 0.00 0.00 2.24
5936 6593 4.307032 ACTGTACTCCCTCCGTAAACTA 57.693 45.455 0.00 0.00 0.00 2.24
5937 6594 3.166560 ACTGTACTCCCTCCGTAAACT 57.833 47.619 0.00 0.00 0.00 2.66
5938 6595 6.699575 TTATACTGTACTCCCTCCGTAAAC 57.300 41.667 0.00 0.00 0.00 2.01
5939 6596 6.891908 AGTTTATACTGTACTCCCTCCGTAAA 59.108 38.462 0.00 0.00 31.99 2.01
5940 6597 6.426587 AGTTTATACTGTACTCCCTCCGTAA 58.573 40.000 0.00 0.00 31.99 3.18
5941 6598 6.006275 AGTTTATACTGTACTCCCTCCGTA 57.994 41.667 0.00 0.00 31.99 4.02
5942 6599 4.864726 AGTTTATACTGTACTCCCTCCGT 58.135 43.478 0.00 0.00 31.99 4.69
5943 6600 6.017275 CAGTAGTTTATACTGTACTCCCTCCG 60.017 46.154 6.84 0.00 39.88 4.63
5944 6601 7.274603 CAGTAGTTTATACTGTACTCCCTCC 57.725 44.000 6.84 0.00 39.88 4.30
5955 6612 8.977267 AGGATCGACTTACAGTAGTTTATACT 57.023 34.615 0.00 0.00 38.44 2.12
5958 6615 8.351461 GCTTAGGATCGACTTACAGTAGTTTAT 58.649 37.037 0.00 0.00 0.00 1.40
5959 6616 7.555554 AGCTTAGGATCGACTTACAGTAGTTTA 59.444 37.037 0.00 0.00 0.00 2.01
5960 6617 6.377712 AGCTTAGGATCGACTTACAGTAGTTT 59.622 38.462 0.00 0.00 0.00 2.66
5961 6618 5.887035 AGCTTAGGATCGACTTACAGTAGTT 59.113 40.000 0.00 0.00 0.00 2.24
5962 6619 5.438833 AGCTTAGGATCGACTTACAGTAGT 58.561 41.667 0.00 0.00 0.00 2.73
5963 6620 6.380095 AAGCTTAGGATCGACTTACAGTAG 57.620 41.667 0.00 0.00 0.00 2.57
5964 6621 7.095313 CGATAAGCTTAGGATCGACTTACAGTA 60.095 40.741 20.44 0.00 44.04 2.74
5965 6622 6.293516 CGATAAGCTTAGGATCGACTTACAGT 60.294 42.308 20.44 0.00 44.04 3.55
5966 6623 6.081049 CGATAAGCTTAGGATCGACTTACAG 58.919 44.000 20.44 0.00 44.04 2.74
5967 6624 5.562307 GCGATAAGCTTAGGATCGACTTACA 60.562 44.000 26.46 0.00 44.04 2.41
5968 6625 4.852650 GCGATAAGCTTAGGATCGACTTAC 59.147 45.833 26.46 10.26 44.04 2.34
5977 6634 1.339929 TGCATCGCGATAAGCTTAGGA 59.660 47.619 25.79 10.92 45.59 2.94
6001 6658 0.523519 TGCAGACAGAGCAGTCGTAG 59.476 55.000 0.00 0.00 43.24 3.51
6051 6712 8.827677 GTTTAAGCAATAGTATGAAACTCCGAT 58.172 33.333 0.00 0.00 39.80 4.18
6052 6713 8.193250 GTTTAAGCAATAGTATGAAACTCCGA 57.807 34.615 0.00 0.00 39.80 4.55


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.